Job ID = 11388938 sra ファイルのダウンロード中... Completed: 924835K bytes transferred in 23 seconds (324621K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Read 16826354 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017457/SRR8198080.sra Written 16826354 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5017457/SRR8198080.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:28:49 16826354 reads; of these: 16826354 (100.00%) were paired; of these: 1049464 (6.24%) aligned concordantly 0 times 14161401 (84.16%) aligned concordantly exactly 1 time 1615489 (9.60%) aligned concordantly >1 times ---- 1049464 pairs aligned concordantly 0 times; of these: 200786 (19.13%) aligned discordantly 1 time ---- 848678 pairs aligned 0 times concordantly or discordantly; of these: 1697356 mates make up the pairs; of these: 1486617 (87.58%) aligned 0 times 129795 (7.65%) aligned exactly 1 time 80944 (4.77%) aligned >1 times 95.58% overall alignment rate Time searching: 00:28:50 Overall time: 00:28:50 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 1680230 / 15912204 = 0.1056 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Thu, 13 Dec 2018 01:00:20: # Command line: callpeak -t SRX5017457.bam -f BAM -g 12100000 -n SRX5017457.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5017457.10 # format = BAM # ChIP-seq file = ['SRX5017457.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 13 Dec 2018 01:00:20: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:00:20: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:00:20: # Command line: callpeak -t SRX5017457.bam -f BAM -g 12100000 -n SRX5017457.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5017457.20 # format = BAM # ChIP-seq file = ['SRX5017457.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 13 Dec 2018 01:00:20: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:00:20: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:00:20: # Command line: callpeak -t SRX5017457.bam -f BAM -g 12100000 -n SRX5017457.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5017457.05 # format = BAM # ChIP-seq file = ['SRX5017457.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 13 Dec 2018 01:00:20: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:00:20: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:00:28: 1000000 INFO @ Thu, 13 Dec 2018 01:00:29: 1000000 INFO @ Thu, 13 Dec 2018 01:00:30: 1000000 INFO @ Thu, 13 Dec 2018 01:00:36: 2000000 INFO @ Thu, 13 Dec 2018 01:00:38: 2000000 INFO @ Thu, 13 Dec 2018 01:00:41: 2000000 INFO @ Thu, 13 Dec 2018 01:00:45: 3000000 INFO @ Thu, 13 Dec 2018 01:00:48: 3000000 INFO @ Thu, 13 Dec 2018 01:00:52: 3000000 INFO @ Thu, 13 Dec 2018 01:00:54: 4000000 INFO @ Thu, 13 Dec 2018 01:00:58: 4000000 INFO @ Thu, 13 Dec 2018 01:01:02: 5000000 INFO @ Thu, 13 Dec 2018 01:01:04: 4000000 INFO @ Thu, 13 Dec 2018 01:01:06: 5000000 INFO @ Thu, 13 Dec 2018 01:01:09: 6000000 INFO @ Thu, 13 Dec 2018 01:01:14: 6000000 INFO @ Thu, 13 Dec 2018 01:01:15: 5000000 INFO @ Thu, 13 Dec 2018 01:01:17: 7000000 INFO @ Thu, 13 Dec 2018 01:01:21: 7000000 INFO @ Thu, 13 Dec 2018 01:01:24: 8000000 INFO @ Thu, 13 Dec 2018 01:01:26: 6000000 INFO @ Thu, 13 Dec 2018 01:01:29: 8000000 INFO @ Thu, 13 Dec 2018 01:01:31: 9000000 INFO @ Thu, 13 Dec 2018 01:01:36: 7000000 INFO @ Thu, 13 Dec 2018 01:01:37: 9000000 INFO @ Thu, 13 Dec 2018 01:01:38: 10000000 INFO @ Thu, 13 Dec 2018 01:01:44: 8000000 INFO @ Thu, 13 Dec 2018 01:01:45: 10000000 INFO @ Thu, 13 Dec 2018 01:01:46: 11000000 INFO @ Thu, 13 Dec 2018 01:01:53: 12000000 INFO @ Thu, 13 Dec 2018 01:01:54: 9000000 INFO @ Thu, 13 Dec 2018 01:01:55: 11000000 INFO @ Thu, 13 Dec 2018 01:02:01: 13000000 INFO @ Thu, 13 Dec 2018 01:02:04: 12000000 INFO @ Thu, 13 Dec 2018 01:02:09: 14000000 INFO @ Thu, 13 Dec 2018 01:02:10: 10000000 INFO @ Thu, 13 Dec 2018 01:02:12: 13000000 INFO @ Thu, 13 Dec 2018 01:02:17: 15000000 INFO @ Thu, 13 Dec 2018 01:02:20: 11000000 INFO @ Thu, 13 Dec 2018 01:02:20: 14000000 INFO @ Thu, 13 Dec 2018 01:02:25: 16000000 INFO @ Thu, 13 Dec 2018 01:02:28: 12000000 INFO @ Thu, 13 Dec 2018 01:02:29: 15000000 INFO @ Thu, 13 Dec 2018 01:02:33: 17000000 INFO @ Thu, 13 Dec 2018 01:02:36: 13000000 INFO @ Thu, 13 Dec 2018 01:02:37: 16000000 INFO @ Thu, 13 Dec 2018 01:02:41: 18000000 INFO @ Thu, 13 Dec 2018 01:02:44: 14000000 INFO @ Thu, 13 Dec 2018 01:02:45: 17000000 INFO @ Thu, 13 Dec 2018 01:02:51: 19000000 INFO @ Thu, 13 Dec 2018 01:02:52: 15000000 INFO @ Thu, 13 Dec 2018 01:02:52: 18000000 INFO @ Thu, 13 Dec 2018 01:03:00: 16000000 INFO @ Thu, 13 Dec 2018 01:03:00: 19000000 INFO @ Thu, 13 Dec 2018 01:03:01: 20000000 INFO @ Thu, 13 Dec 2018 01:03:08: 20000000 INFO @ Thu, 13 Dec 2018 01:03:08: 17000000 INFO @ Thu, 13 Dec 2018 01:03:10: 21000000 INFO @ Thu, 13 Dec 2018 01:03:16: 21000000 INFO @ Thu, 13 Dec 2018 01:03:17: 18000000 INFO @ Thu, 13 Dec 2018 01:03:21: 22000000 INFO @ Thu, 13 Dec 2018 01:03:24: 22000000 INFO @ Thu, 13 Dec 2018 01:03:25: 19000000 INFO @ Thu, 13 Dec 2018 01:03:31: 23000000 INFO @ Thu, 13 Dec 2018 01:03:32: 23000000 INFO @ Thu, 13 Dec 2018 01:03:34: 20000000 INFO @ Thu, 13 Dec 2018 01:03:39: 24000000 INFO @ Thu, 13 Dec 2018 01:03:40: 24000000 INFO @ Thu, 13 Dec 2018 01:03:43: 21000000 INFO @ Thu, 13 Dec 2018 01:03:47: 25000000 INFO @ Thu, 13 Dec 2018 01:03:49: 25000000 INFO @ Thu, 13 Dec 2018 01:03:51: 22000000 INFO @ Thu, 13 Dec 2018 01:03:54: 26000000 INFO @ Thu, 13 Dec 2018 01:03:58: 26000000 INFO @ Thu, 13 Dec 2018 01:03:59: 23000000 INFO @ Thu, 13 Dec 2018 01:04:02: 27000000 INFO @ Thu, 13 Dec 2018 01:04:07: 27000000 INFO @ Thu, 13 Dec 2018 01:04:07: 24000000 INFO @ Thu, 13 Dec 2018 01:04:10: 28000000 INFO @ Thu, 13 Dec 2018 01:04:16: 25000000 INFO @ Thu, 13 Dec 2018 01:04:16: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 01:04:16: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 01:04:16: #1 total tags in treatment: 14105871 INFO @ Thu, 13 Dec 2018 01:04:16: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:04:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:04:16: #1 tags after filtering in treatment: 9286721 INFO @ Thu, 13 Dec 2018 01:04:16: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 13 Dec 2018 01:04:16: #1 finished! INFO @ Thu, 13 Dec 2018 01:04:16: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:04:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:04:17: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 01:04:17: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Thu, 13 Dec 2018 01:04:17: Process for pairing-model is terminated! cat: SRX5017457.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017457.05_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX5017457.05_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX5017457.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Thu, 13 Dec 2018 01:04:18: 28000000 INFO @ Thu, 13 Dec 2018 01:04:24: 26000000 INFO @ Thu, 13 Dec 2018 01:04:26: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 01:04:26: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 01:04:26: #1 total tags in treatment: 14105871 INFO @ Thu, 13 Dec 2018 01:04:26: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:04:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:04:27: #1 tags after filtering in treatment: 9286721 INFO @ Thu, 13 Dec 2018 01:04:27: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 13 Dec 2018 01:04:27: #1 finished! INFO @ Thu, 13 Dec 2018 01:04:27: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:04:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:04:27: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 01:04:27: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Thu, 13 Dec 2018 01:04:27: Process for pairing-model is terminated! cat: SRX5017457.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017457.20_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX5017457.20_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX5017457.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Thu, 13 Dec 2018 01:04:31: 27000000 INFO @ Thu, 13 Dec 2018 01:04:38: 28000000 INFO @ Thu, 13 Dec 2018 01:04:45: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 01:04:45: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 01:04:45: #1 total tags in treatment: 14105871 INFO @ Thu, 13 Dec 2018 01:04:45: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:04:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:04:45: #1 tags after filtering in treatment: 9286721 INFO @ Thu, 13 Dec 2018 01:04:45: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 13 Dec 2018 01:04:45: #1 finished! INFO @ Thu, 13 Dec 2018 01:04:45: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:04:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:04:46: #2 number of paired peaks: 0 WARNING @ Thu, 13 Dec 2018 01:04:46: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Thu, 13 Dec 2018 01:04:46: Process for pairing-model is terminated! cat: SRX5017457.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX5017457.10_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX5017457.10_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX5017457.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。